9OHZ | pdb_00009ohz

Crystal structure of CD1a presenting ganglioside GD3

• PDB DOI: https://doi.org/10.2210/pdb9OHZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-05-05 Released: 2025-11-19 
• Deposition Author(s): Cao, T.P., Ciacchi, L., Rossjohn, J., Shahine, A.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CD1a presenting ganglioside GD3

Cao, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 46.08 kDa 
• Atom Count: 3,208 
• Modeled Residue Count: 375 
• Deposited Residue Count: 391 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD1a	A	285	Homo sapiens	Mutation(s): 1  Gene Names: CD1A
UniProt & NIH Common Fund Data Resources
Find proteins for P06126 (Homo sapiens) Explore P06126  Go to UniProtKB:  P06126
PHAROS:  P06126 GTEx:  ENSG00000158477
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P06126-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	106	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CB9 (Subject of Investigation/LOI)	D [auth A]	N-{(2S,3R)-1-[(4-O-beta-D-galactopyranosyl-beta-D-glucopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}tetracosanamide C54 H105 N O13 JRPWXSMBCYEJCN-DJSCMYBVSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.392	α = 90
b = 90.35	β = 90
c = 107.445	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Cao, T.P., Ciacchi, L., Rossjohn, J., Shahine, A.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DE210101031

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release